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The basic idea of the game is to create rectangles which have to be two-by-three blocks or larger to clear them from the grid. Blocks cannot be placed on top of blocks of the same color that are already on the grid, but they can be placed on top of blocks of any other color which causes the different blocks on the grid to disappear.

The game incorporates three main game modes: Puzzle, Wipeout and Marathon. There is also a fourth game mode called "Max's Mystical Muddle" which is opened up by completing all of the puzzles in Puzzle mode.

It's Mr. Pants was developed by Rare, which, during much of the game's production, was a second-party developer for Nintendo. Rare was responsible for creating games in Nintendo's long-running Donkey Kong franchise. Early in the course of development, the game went through several name changes including Splonge, Nutcracker, Animal Cracker, and Sunflower.[3] It was eventually presented by Rare at the Electronic Entertainment Expo 2001 as Donkey Kong Coconut Crackers, one of four titles for Nintendo's GBA handheld game console.[4][5] In September 2002, Nintendo announced it had sold off its 49 percent stake in Rare back to latter company; Rare subsequently sold its entire company to Microsoft Studios.[6] The Donkey Kongintellectual property for which Nintendo held Rare responsible, defaulted back to Nintendo, forcing Rare to abandon this theme for the then-upcoming puzzle game.[3][7] On August 11, 2003, Microsoft announced their partnership with publisher THQ for distributing Rare's GBA titles, including the newly revealed It's Mr. Pants, set for an early 2004 release.[8]

It's Mr. Pants was originally conceived by Rare veterans Tim Stamper and Gregg Mayles.[7] The game was chiefly designed by Justin Cook and Paul Machacek.[7][9] Cook, who credits himself for creating two-thirds of the game's levels, described It's Mr. Pants as "just a solid puzzle game", stating, "We knew that it wasn't a big 'wow' game, but the playability was there." After the breakdown of its relationship with Nintendo, Rare chose to rebrand the game with the company's online mascot Mr. Pants, which the latter company used in its website surveys collectively called "The Pantsboard".[3][10][11] The character Mr. Pants was originally illustrated by artist Leigh Loveday, but the design was implemented into the game by Ryan Stevenson.[12] Mayles recounted that the "childish" visual style used in It's Mr. Pants was accomplished by having the right-handed artists draw with their left hands to intentionally make the illustrations appear "genuinely bad".[3]

The Donkey Kong Coconut Crackers incarnation of the game featured the ability to switch between top-down 2D graphics and a 3Disometric layout. According to the developer, the isometric perspective was scrapped due to "consistency issues" when swapping between the two views, due to it being awkward seeing where puzzle pieces near the back of the board were, and finally because it "just didn't look as nice" as they had hoped.[13] When It's Mr. Pants was first revealed as Donkey Kong Coconut Crackers, the game was intended to be multiplayer for up to four individuals using the GBA Game Link Cable.[4] Rare had experimented with various multiplayer modes during the game's development, but ultimately released the game as single-player only.[12] Once the game was submitted to THQ, the publisher requested a few slight changes be made. For instance, the "Crayon Snake" that circles around the board in Marathon Mode was originally called the "trouser snake".[7]It's Mr. Pants was also in development for the Gizmondo handheld, but was cancelled due to the console's failure.[14]